Thanks for the replies guys. I am going to look at it again this aftermoon.
Yesterday I stepped the motor round manually on a power supply by switching the phases by hand. It stepped round in 30' increments as expected, and needed 12 steps to complete 1 mechanical revolution. When I have it running on the driver board though, it seems to have 24 steps. This is where the problem occurs. There are 4 equi-spaced positions where the motor appears to stop between steps, and the Hall signals are '000, so when it comes to starting again, there is no output. Moving the motor one notch, and it works fine.
Any ideas welcomed. Please feel free to state the obvious, this is my first BLDC controller, so i wont be offended!